Contacts of the helix formed by residues 302 - 309 (chain A) in PDB entry 4BBZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A SER* 6.3 3.1 - - - -
294A VAL* 4.0 13.4 - - + +
301A ASP* 1.3 86.3 + - - +
303A PRO* 1.3 66.1 - - + +
304A ASP* 3.2 22.9 - - - +
305A ILE* 3.0 41.3 + - + +
306A LEU* 3.4 8.7 + - - +
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Residues in contact with PRO 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.4 2.0 - - + -
209A LEU* 3.6 19.6 - - + +
227A PHE* 3.3 38.5 - - + -
233A VAL* 4.0 26.5 - - + -
294A VAL* 4.3 10.8 - - + -
299A LEU* 4.1 15.5 - - + -
301A ASP 3.2 7.8 - - - +
302A MET* 1.3 85.8 - - + +
304A ASP* 1.3 65.4 + - - +
305A ILE 3.2 0.2 - - - -
306A LEU* 3.8 4.9 - - + -
307A LEU 3.0 19.4 + - - -
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Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A PHE* 3.8 8.6 - - + -
228A ASN* 5.9 4.9 - - + -
302A MET* 3.4 34.7 - - - +
303A PRO* 1.3 78.2 - - - +
305A ILE* 1.3 64.8 + - - +
307A LEU* 3.8 4.8 - - - +
308A GLU* 3.0 29.6 + - - +
408A LYS* 4.7 7.3 + - - +
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Residues in contact with ILE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A ASP* 3.9 24.5 - - - +
302A MET* 3.0 36.5 + - + +
304A ASP* 1.3 81.5 - - - +
306A LEU* 1.3 61.5 + - + +
308A GLU* 3.2 4.9 + - - +
309A LEU* 2.9 56.5 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.0 25.8 - - + +
299A LEU* 4.0 26.7 - - + -
300A THR* 4.6 11.7 - - - +
301A ASP* 3.9 31.4 - - + +
302A MET 3.4 9.3 + - - +
303A PRO* 3.4 6.0 + - + +
305A ILE* 1.3 76.8 - - + +
307A LEU* 1.3 61.1 + - - +
309A LEU 3.3 0.7 + - - -
310A GLY 3.0 4.3 + - - -
311A GLN* 2.7 61.4 + - + +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.6 3.4 - - + +
227A PHE* 3.5 24.9 - - + -
228A ASN* 4.7 8.7 - - + +
303A PRO 3.0 17.6 + - - +
304A ASP* 3.8 5.2 - - - +
306A LEU* 1.3 73.6 - - - +
308A GLU* 1.3 66.4 + - - +
309A LEU 3.1 1.0 + - - -
310A GLY* 3.1 9.9 + - - -
312A PHE* 3.5 24.0 - - + -
405A PHE* 4.0 31.0 - - + +
408A LYS* 3.5 42.2 - - + +
409A PHE* 3.9 14.4 - - + +
412A TRP* 3.9 5.0 + - - -
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Residues in contact with GLU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASP 3.0 19.9 + - - +
305A ILE* 3.2 6.9 + - + +
307A LEU* 1.3 77.3 - - - +
309A LEU* 1.3 72.6 + - + +
310A GLY 3.4 0.7 + - - -
408A LYS* 2.9 39.5 + - - +
412A TRP* 3.9 12.1 + - - -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A ILE* 2.9 37.5 + - + +
306A LEU* 4.2 1.1 - - - +
308A GLU* 1.3 92.5 - - + +
310A GLY* 1.3 63.5 + - - +
311A GLN* 3.3 24.4 + - + +
412A TRP* 3.5 17.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il